runSpatialEnrich#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_enrichment.R#L1292

Description#

Function to calculate gene signature enrichment scores per spatial position using an enrichment test.

Usage#

runSpatialEnrich(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  enrich_method = c("PAGE", "rank", "hypergeometric"),
  sign_matrix,
  expression_values = c("normalized", "scaled", "custom"),
  min_overlap_genes = 5,
  reverse_log_scale = TRUE,
  logbase = 2,
  p_value = FALSE,
  n_times = 1000,
  rbp_p = 0.99,
  num_agg = 100,
  max_block = 2e+07,
  top_percentage = 5,
  output_enrichment = c("original", "zscore"),
  name = NULL,
  verbose = TRUE,
  return_gobject = TRUE
)

Arguments#

Argument

Description

gobject

Giotto object

spat_unit

spatial unit

feat_type

feature type

enrich_method

method for gene signature enrichment calculation

sign_matrix

Matrix of signature genes for each cell type / process

expression_values

expression values to use

min_overlap_genes

minimum number of overlapping genes in sign_matrix required to calculate enrichment (PAGE)

reverse_log_scale

reverse expression values from log scale

logbase

log base to use if reverse_log_scale = TRUE

p_value

calculate p-value (default = FALSE)

n_times

(page/rank) number of permutation iterations to calculate p-value

rbp_p

(rank) fractional binarization threshold (default = 0.99)

num_agg

(rank) number of top genes to aggregate (default = 100)

max_block

number of lines to process together (default = 20e6)

top_percentage

(hyper) percentage of cells that will be considered to have gene expression with matrix binarization

output_enrichment

how to return enrichment output

name

to give to spatial enrichment results, default = PAGE

verbose

be verbose

return_gobject

return giotto object

Details#

For details see the individual functions:

  • PAGE: list(list(“runPAGEEnrich?))

  • Rank: list(list(“runRankEnrich?))

  • Hypergeometric: list(list(“runHyperGeometricEnrich?))

Value#

Giotto object or enrichment results if return_gobject = FALSE